Peter Lerner said the banks, closed in the isolated Palestinian enclave over a shortage of cash to pay salaries, are to receive the funds within a few days.
Israeli Defense Minister Ehud Barak approved the transfer of funds through the Israel-blockaded border following a request by Salam Fayyad, who heads the internationally acknowledged government in the Palestinian National Authority (PNA).
Fayyad said the funds were needed to pay some 70,000 public sector workers.
The majority of the workers were employed in the public sector prior to the take over of the Gaza Strip from the more moderate Fatah by the radical Hamas movement in June 2007.
Hamas and Israel agreed to an Egyptian-brokered truce in June but Tel Aviv virtually closed the border in early November after militants fired rockets onto Israeli border towns in response to raids on the Gaza Strip by Israeli troops.